Abstract
BackgroundAs an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation.ResultsThe overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation.ConclusionsDNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.
Highlights
As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNAdependent biological processes and plays a role during development and differentiation of multicellular organisms
Morphological and histochemical changes in P. trichocarpa stems To verify the rationality of the classification of the main stems of poplar into different developmental stages using the plastochron indices method, we determined the developmental stages of internodes two (IN2), four (IN4), and eight (IN8) using histochemical staining
Because the vascular bundles in IN2 comprised mainly of primary xylem and phloem tissues that were formed from procambial cells, toluidine blue-O and phloroglucinol-HCl staining in the cross sections of IN2 were nearly undetectable (Fig. 1b and c), and calcofluor white staining in IN2 sections was weak (Fig. 1d)
Summary
As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNAdependent biological processes and plays a role during development and differentiation of multicellular organisms. There is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. Wood originates from vascular cambium, the secondary meristem located between tree barks and woody trunks; vascular cambium produces undifferentiated xylem mother cells inwardly and bark cells outwardly. For this reason, cambium activity is the most important determining factor for wood accumulation. The contribution of epigenetic regulation during this process is still unclear
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